rs11720452

chr3-21207150-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000634947.1(ENSG00000282987):n.370+17538G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,100 control chromosomes in the GnomAD database, including 5,910 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5910 hom., cov: 33)
• Consequence: ENST00000634947.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376988	XR_940646.3	n.545-3848C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634947.1	n.370+17538G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37421 AN: 151984 Hom.: 5911 Cov.: 33

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.246 AC: 37415 AN: 152100 Hom.: 5910 Cov.: 33 AF XY: 0.239 AC XY: 17783 AN XY: 74348

Gnomad4 AFR AF: 0.0685

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.255

Alfa AF: 0.339 Hom.: 15519

Bravo AF: 0.233

Asia WGS AF: 0.120 AC: 416 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
Cadd	Benign	18
Dann	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11720452; hg19: chr3-21248642;